P281424/AMR
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v1.8.0 as accepted by CRAN

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dr. M.S. (Matthijs) Berends 2022-01-07 16:27:13 +01:00
parent 25cef46c59
commit f5dcf0ad58
10 changed files with 5 additions and 14 deletions
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1
.Rbuildignore
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@ -32,3 +32,4 @@
^vignettes/resistance_predict.Rmd$ ^vignettes/resistance_predict.Rmd$
^vignettes/SPSS.Rmd$ ^vignettes/SPSS.Rmd$
^vignettes/WHONET.Rmd$ ^vignettes/WHONET.Rmd$
^logo.svg$

4
DESCRIPTION
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@ -66,7 +66,7 @@ Authors@R: c(
person(given = "Anthony", person(given = "Anthony",
family = "Underwood", family = "Underwood",
role = "ctb", role = "ctb",
comment = c(ORCID = "0000-0002-8547-427"))) comment = c(ORCID = "0000-0002-8547-4277")))
Depends: R (>= 3.0.0) Depends: R (>= 3.0.0)
Enhances: Enhances:
cleaner, cleaner,
@ -84,7 +84,7 @@ Suggests:
tinytest, tinytest,
xml2 xml2
VignetteBuilder: knitr,rmarkdown VignetteBuilder: knitr,rmarkdown
URL: https://msberends.github.io/AMR, https://github.com/msberends/AMR URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE License: GPL-2 | file LICENSE
Encoding: UTF-8 Encoding: UTF-8

2
R/ab.R
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@ -48,8 +48,6 @@
#' @section Source: #' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/} #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#' #'
#' WHONET 2019 software: \url{http://www.whonet.org/software.html}
#'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases ab #' @aliases ab
#' @return A [character] [vector] with additional class [`ab`] #' @return A [character] [vector] with additional class [`ab`]

2
R/data.R
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@ -69,8 +69,6 @@
#' * <https://github.com/msberends/AMR/raw/main/data/antivirals.rda> #' * <https://github.com/msberends/AMR/raw/main/data/antivirals.rda>
#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/> #' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
#' #'
#' WHONET 2019 software: <http://www.whonet.org/software.html>
#'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm> #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
#' @inheritSection AMR Reference Data Publicly Available #' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection WHOCC WHOCC #' @inheritSection WHOCC WHOCC

2
README.md
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@ -4,7 +4,7 @@
![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main) ![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main)
[![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr) [![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
[![Codecov](https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=main) [![Codecov](https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/msberends/AMR?branch=main)
<img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center" height="300px" /> <img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center" height="300px" />

2
cran-comments.md
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@ -1 +1 @@
* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, following 15 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible. * This package has a data folder size of ~1.7 MB, which might return a NOTE on some R CMD CHECKs. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, as it has been in the 16 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.

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data-raw/AMR_latest.tar.gz
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2
man/ab_property.Rd
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@ -107,8 +107,6 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
WHONET 2019 software: \url{http://www.whonet.org/software.html}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }

2
man/antibiotics.Rd
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@ -44,8 +44,6 @@ An object of class \code{data.frame} with 102 rows and 9 columns.
\source{ \source{
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
WHONET 2019 software: \url{http://www.whonet.org/software.html}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }
\usage{ \usage{

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man/as.ab.Rd
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@ -44,8 +44,6 @@ Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} fun
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/} World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
WHONET 2019 software: \url{http://www.whonet.org/software.html}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }